## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  2:       1    ORF4 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  3:       1    ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  4:       1    ORF7 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  5:       1    ORF9 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  6:       1   ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  7:       1   ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  8:       1   ORF20 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  9:       1   ORF21 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10:       1   ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11:       1   ORF31 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12:       1   ORF34 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 13:       1   ORF38 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 14:       1   ORF50 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 15:       1   ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 16:       1   ORF56 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 17:       1   ORF61 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 18:       1   ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 19:       1  NOIR_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 20:       1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 21:       1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 22:       1   ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 23:       1  NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 24:       2    ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25:       2    ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26:       2    ORF8 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 27:       2   ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 28:       2   ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 29:       2   ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 30:       2   ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 31:       2   ORF22 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 32:       2   ORF23 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 33:       2   ORF24 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 34:       2   ORF25 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 35:       2   ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 36:       2   ORF27 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 37:       2   ORF28 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 38:       2   ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 39:       2   ORF32 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 40:       2   ORF33 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 41:       2 ORF35.5 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 42:       2   ORF36 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 43:       2   ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 44:       2   ORF39 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 45:       2     CTO 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 46:       2   ORF40 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 47:       2   ORF42 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 48:       2   ORF43 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 49:       2   ORF44 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 50:       2   ORF46 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 51:       2   ORF49 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 52:       2   ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 53:       2   ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 54:       2   ORF58 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 55:       2   ORF59 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 56:       2   ORF62 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 57:       2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 58:       2   ORF68 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 59:       2   ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 60:       2   ORF74 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 61:       2   ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 62:       3    ORF6 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 63:       3   ORF70 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 64:       4   ORF12 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 65:       4   ORF13 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 66:       4   ORF15 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 67:       4   ORF16 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 68:       4   ORF35 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 69:       4   ORF41 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 70:       4   ORF45 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 71:       4   ORF48 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 72:       4   ORF52 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 73:       4   ORF54 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 74:       4   ORF57 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 75:       4   ORF60 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 76:       4   ORF71 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 77:       4   ORF72 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 78:       5 ORF64_1 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 79:       5   ORF75 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004437298 -1.8423439 0.9718909 0.80502549
##  2: 0.004437298 -1.8423439 0.9718909 0.80502549
##  3: 0.004437298 -1.8423439 0.9718909 0.80502549
##  4: 0.004437298 -1.8423439 0.9718909 0.80502549
##  5: 0.004437298 -1.8423439 0.9718909 0.80502549
##  6: 0.004437298 -1.8423439 0.9718909 0.80502549
##  7: 0.004437298 -1.8423439 0.9718909 0.80502549
##  8: 0.004437298 -1.8423439 0.9718909 0.80502549
##  9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.004437298 -1.8423439 0.9718909 0.80502549
## 13: 0.004437298 -1.8423439 0.9718909 0.80502549
## 14: 0.004437298 -1.8423439 0.9718909 0.80502549
## 15: 0.004437298 -1.8423439 0.9718909 0.80502549
## 16: 0.004437298 -1.8423439 0.9718909 0.80502549
## 17: 0.004437298 -1.8423439 0.9718909 0.80502549
## 18: 0.004437298 -1.8423439 0.9718909 0.80502549
## 19: 0.004437298 -1.8423439 0.9718909 0.80502549
## 20: 0.004437298 -1.8423439 0.9718909 0.80502549
## 21: 0.004437298 -1.8423439 0.9718909 0.80502549
## 22: 0.004437298 -1.8423439 0.9718909 0.80502549
## 23: 0.004437298 -1.8423439 0.9718909 0.80502549
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.005027291 -1.1453678 0.6808478 0.04001638
## 27: 0.005027291 -1.1453678 0.6808478 0.04001638
## 28: 0.005027291 -1.1453678 0.6808478 0.04001638
## 29: 0.005027291 -1.1453678 0.6808478 0.04001638
## 30: 0.005027291 -1.1453678 0.6808478 0.04001638
## 31: 0.005027291 -1.1453678 0.6808478 0.04001638
## 32: 0.005027291 -1.1453678 0.6808478 0.04001638
## 33: 0.005027291 -1.1453678 0.6808478 0.04001638
## 34: 0.005027291 -1.1453678 0.6808478 0.04001638
## 35: 0.005027291 -1.1453678 0.6808478 0.04001638
## 36: 0.005027291 -1.1453678 0.6808478 0.04001638
## 37: 0.005027291 -1.1453678 0.6808478 0.04001638
## 38: 0.005027291 -1.1453678 0.6808478 0.04001638
## 39: 0.005027291 -1.1453678 0.6808478 0.04001638
## 40: 0.005027291 -1.1453678 0.6808478 0.04001638
## 41: 0.005027291 -1.1453678 0.6808478 0.04001638
## 42: 0.005027291 -1.1453678 0.6808478 0.04001638
## 43: 0.005027291 -1.1453678 0.6808478 0.04001638
## 44: 0.005027291 -1.1453678 0.6808478 0.04001638
## 45: 0.005027291 -1.1453678 0.6808478 0.04001638
## 46: 0.005027291 -1.1453678 0.6808478 0.04001638
## 47: 0.005027291 -1.1453678 0.6808478 0.04001638
## 48: 0.005027291 -1.1453678 0.6808478 0.04001638
## 49: 0.005027291 -1.1453678 0.6808478 0.04001638
## 50: 0.005027291 -1.1453678 0.6808478 0.04001638
## 51: 0.005027291 -1.1453678 0.6808478 0.04001638
## 52: 0.005027291 -1.1453678 0.6808478 0.04001638
## 53: 0.005027291 -1.1453678 0.6808478 0.04001638
## 54: 0.005027291 -1.1453678 0.6808478 0.04001638
## 55: 0.005027291 -1.1453678 0.6808478 0.04001638
## 56: 0.005027291 -1.1453678 0.6808478 0.04001638
## 57: 0.005027291 -1.1453678 0.6808478 0.04001638
## 58: 0.005027291 -1.1453678 0.6808478 0.04001638
## 59: 0.005027291 -1.1453678 0.6808478 0.04001638
## 60: 0.005027291 -1.1453678 0.6808478 0.04001638
## 61: 0.005027291 -1.1453678 0.6808478 0.04001638
## 62: 0.004876780 -1.6233205 0.9970391 0.31825293
## 63: 0.004876780 -1.6233205 0.9970391 0.31825293
## 64: 0.004864578 -1.8164413 1.1545088 0.27283204
## 65: 0.004864578 -1.8164413 1.1545088 0.27283204
## 66: 0.004864578 -1.8164413 1.1545088 0.27283204
## 67: 0.004864578 -1.8164413 1.1545088 0.27283204
## 68: 0.004864578 -1.8164413 1.1545088 0.27283204
## 69: 0.004864578 -1.8164413 1.1545088 0.27283204
## 70: 0.004864578 -1.8164413 1.1545088 0.27283204
## 71: 0.004864578 -1.8164413 1.1545088 0.27283204
## 72: 0.004864578 -1.8164413 1.1545088 0.27283204
## 73: 0.004864578 -1.8164413 1.1545088 0.27283204
## 74: 0.004864578 -1.8164413 1.1545088 0.27283204
## 75: 0.004864578 -1.8164413 1.1545088 0.27283204
## 76: 0.004864578 -1.8164413 1.1545088 0.27283204
## 77: 0.004864578 -1.8164413 1.1545088 0.27283204
## 78: 0.004541086 -0.4455417 1.1235184 0.24166784
## 79: 0.004541086 -0.4455417 1.1235184 0.24166784
##           se.bp          v         c       pchi

## [1] "ORF67_1" "ORF32"   "ORF58"   "ORF33"   "ORF35.5" "ORF25"   "ORF27"  
## [8] "ORF62"
## [1] 8
## [1] "ORF64_1" "ORF75"
## [1] 2

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  2:       1    ORF4 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  3:       1    ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  4:       1    ORF7 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  5:       1    ORF9 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  6:       1   ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  7:       1   ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  8:       1   ORF20 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  9:       1   ORF21 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10:       1   ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11:       1   ORF31 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12:       1   ORF34 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 13:       1   ORF38 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 14:       1   ORF50 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 15:       1   ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 16:       1   ORF56 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 17:       1   ORF61 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 18:       1   ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 19:       1  NOIR_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 20:       1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 21:       1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 22:       1   ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 23:       1  NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 24:       2    ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25:       2    ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26:       2   ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 27:       2   ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 28:       2   ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 29:       2   ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 30:       2   ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 31:       2   ORF28 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 32:       2   ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 33:       2   ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 34:       2   ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 35:       2   ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 36:       2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 37:       2   ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 38:       2   ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 39:       3    ORF6 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 40:       3   ORF70 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 41:       4    ORF8 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 42:       4   ORF22 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 43:       4   ORF23 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 44:       4   ORF24 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 45:       4   ORF25 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 46:       4   ORF27 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 47:       4   ORF32 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 48:       4   ORF33 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 49:       4 ORF35.5 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 50:       4   ORF36 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 51:       4   ORF39 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 52:       4     CTO 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 53:       4   ORF40 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 54:       4   ORF42 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 55:       4   ORF43 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 56:       4   ORF44 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 57:       4   ORF46 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 58:       4   ORF49 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 59:       4   ORF58 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 60:       4   ORF59 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 61:       4   ORF62 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 62:       4   ORF68 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 63:       4   ORF74 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 64:       5   ORF12 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 65:       5   ORF13 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 66:       5   ORF15 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 67:       5   ORF16 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 68:       5   ORF35 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 69:       5   ORF41 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 70:       5   ORF45 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 71:       5   ORF48 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 72:       5   ORF52 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 73:       5   ORF54 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 74:       5   ORF57 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 75:       5   ORF60 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 76:       5   ORF71 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 77:       5   ORF72 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 78:       6 ORF64_1 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 79:       6   ORF75 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004437298 -1.8423439 0.9718909 0.80502549
##  2: 0.004437298 -1.8423439 0.9718909 0.80502549
##  3: 0.004437298 -1.8423439 0.9718909 0.80502549
##  4: 0.004437298 -1.8423439 0.9718909 0.80502549
##  5: 0.004437298 -1.8423439 0.9718909 0.80502549
##  6: 0.004437298 -1.8423439 0.9718909 0.80502549
##  7: 0.004437298 -1.8423439 0.9718909 0.80502549
##  8: 0.004437298 -1.8423439 0.9718909 0.80502549
##  9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.004437298 -1.8423439 0.9718909 0.80502549
## 13: 0.004437298 -1.8423439 0.9718909 0.80502549
## 14: 0.004437298 -1.8423439 0.9718909 0.80502549
## 15: 0.004437298 -1.8423439 0.9718909 0.80502549
## 16: 0.004437298 -1.8423439 0.9718909 0.80502549
## 17: 0.004437298 -1.8423439 0.9718909 0.80502549
## 18: 0.004437298 -1.8423439 0.9718909 0.80502549
## 19: 0.004437298 -1.8423439 0.9718909 0.80502549
## 20: 0.004437298 -1.8423439 0.9718909 0.80502549
## 21: 0.004437298 -1.8423439 0.9718909 0.80502549
## 22: 0.004437298 -1.8423439 0.9718909 0.80502549
## 23: 0.004437298 -1.8423439 0.9718909 0.80502549
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.005027291 -1.1453678 0.6808478 0.04001638
## 27: 0.005027291 -1.1453678 0.6808478 0.04001638
## 28: 0.005027291 -1.1453678 0.6808478 0.04001638
## 29: 0.005027291 -1.1453678 0.6808478 0.04001638
## 30: 0.005027291 -1.1453678 0.6808478 0.04001638
## 31: 0.005027291 -1.1453678 0.6808478 0.04001638
## 32: 0.005027291 -1.1453678 0.6808478 0.04001638
## 33: 0.005027291 -1.1453678 0.6808478 0.04001638
## 34: 0.005027291 -1.1453678 0.6808478 0.04001638
## 35: 0.005027291 -1.1453678 0.6808478 0.04001638
## 36: 0.005027291 -1.1453678 0.6808478 0.04001638
## 37: 0.005027291 -1.1453678 0.6808478 0.04001638
## 38: 0.005027291 -1.1453678 0.6808478 0.04001638
## 39: 0.004876780 -1.6233205 0.9970391 0.31825293
## 40: 0.004876780 -1.6233205 0.9970391 0.31825293
## 41: 0.004864578 -1.8164413 1.1545088 0.27283204
## 42: 0.004864578 -1.8164413 1.1545088 0.27283204
## 43: 0.004864578 -1.8164413 1.1545088 0.27283204
## 44: 0.004864578 -1.8164413 1.1545088 0.27283204
## 45: 0.004864578 -1.8164413 1.1545088 0.27283204
## 46: 0.004864578 -1.8164413 1.1545088 0.27283204
## 47: 0.004864578 -1.8164413 1.1545088 0.27283204
## 48: 0.004864578 -1.8164413 1.1545088 0.27283204
## 49: 0.004864578 -1.8164413 1.1545088 0.27283204
## 50: 0.004864578 -1.8164413 1.1545088 0.27283204
## 51: 0.004864578 -1.8164413 1.1545088 0.27283204
## 52: 0.004864578 -1.8164413 1.1545088 0.27283204
## 53: 0.004864578 -1.8164413 1.1545088 0.27283204
## 54: 0.004864578 -1.8164413 1.1545088 0.27283204
## 55: 0.004864578 -1.8164413 1.1545088 0.27283204
## 56: 0.004864578 -1.8164413 1.1545088 0.27283204
## 57: 0.004864578 -1.8164413 1.1545088 0.27283204
## 58: 0.004864578 -1.8164413 1.1545088 0.27283204
## 59: 0.004864578 -1.8164413 1.1545088 0.27283204
## 60: 0.004864578 -1.8164413 1.1545088 0.27283204
## 61: 0.004864578 -1.8164413 1.1545088 0.27283204
## 62: 0.004864578 -1.8164413 1.1545088 0.27283204
## 63: 0.004864578 -1.8164413 1.1545088 0.27283204
## 64: 0.004541086 -0.4455417 1.1235184 0.24166784
## 65: 0.004541086 -0.4455417 1.1235184 0.24166784
## 66: 0.004541086 -0.4455417 1.1235184 0.24166784
## 67: 0.004541086 -0.4455417 1.1235184 0.24166784
## 68: 0.004541086 -0.4455417 1.1235184 0.24166784
## 69: 0.004541086 -0.4455417 1.1235184 0.24166784
## 70: 0.004541086 -0.4455417 1.1235184 0.24166784
## 71: 0.004541086 -0.4455417 1.1235184 0.24166784
## 72: 0.004541086 -0.4455417 1.1235184 0.24166784
## 73: 0.004541086 -0.4455417 1.1235184 0.24166784
## 74: 0.004541086 -0.4455417 1.1235184 0.24166784
## 75: 0.004541086 -0.4455417 1.1235184 0.24166784
## 76: 0.004541086 -0.4455417 1.1235184 0.24166784
## 77: 0.004541086 -0.4455417 1.1235184 0.24166784
## 78: 0.005235761 -1.1178069 0.8390202 0.58404011
## 79: 0.005235761 -1.1178069 0.8390202 0.58404011
##           se.bp          v         c       pchi

## [1] "ORF67_1" "ORF9"    "ORF73"   "ORF32"   "ORF62"   "ORF45"
## [1] 6
##  [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF45" "ORF48" "ORF52"
## [10] "ORF54" "ORF57" "ORF60" "ORF71" "ORF72"
## [1] 14

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  2:       1    ORF4 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  3:       1    ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  4:       1    ORF7 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  5:       1    ORF9 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  6:       1   ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  7:       1   ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  8:       1   ORF20 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  9:       1   ORF21 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10:       1   ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11:       1   ORF31 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12:       1   ORF34 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 13:       1   ORF38 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 14:       1   ORF50 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 15:       1   ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 16:       1   ORF56 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 17:       1   ORF61 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 18:       1   ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 19:       1  NOIR_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 20:       1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 21:       1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 22:       1   ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 23:       1  NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 24:       2    ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25:       2    ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26:       2   ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 27:       2   ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 28:       2   ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 29:       2   ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 30:       2   ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 31:       2   ORF28 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 32:       2   ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 33:       2   ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 34:       2   ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 35:       2   ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 36:       2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 37:       2   ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 38:       2   ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 39:       3    ORF6 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 40:       3   ORF70 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 41:       4    ORF8 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 42:       4   ORF22 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 43:       4   ORF23 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 44:       4   ORF24 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 45:       4   ORF25 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 46:       4   ORF27 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 47:       4   ORF32 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 48:       4   ORF33 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 49:       4 ORF35.5 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 50:       4   ORF36 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 51:       4   ORF39 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 52:       4     CTO 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 53:       4   ORF40 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 54:       4   ORF42 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 55:       4   ORF43 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 56:       4   ORF44 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 57:       4   ORF46 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 58:       4   ORF49 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 59:       4   ORF58 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 60:       4   ORF59 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 61:       4   ORF62 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 62:       4   ORF68 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 63:       4   ORF74 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 64:       5   ORF12 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 65:       5   ORF13 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 66:       5   ORF15 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 67:       5   ORF16 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 68:       5   ORF35 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 69:       5   ORF41 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 70:       5   ORF48 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 71:       5   ORF52 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 72:       5   ORF54 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 73:       5   ORF57 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 74:       5   ORF60 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 75:       5   ORF71 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 76:       5   ORF72 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 77:       6   ORF45 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 78:       7 ORF64_1 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 79:       7   ORF75 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004437298 -1.8423439 0.9718909 0.80502549
##  2: 0.004437298 -1.8423439 0.9718909 0.80502549
##  3: 0.004437298 -1.8423439 0.9718909 0.80502549
##  4: 0.004437298 -1.8423439 0.9718909 0.80502549
##  5: 0.004437298 -1.8423439 0.9718909 0.80502549
##  6: 0.004437298 -1.8423439 0.9718909 0.80502549
##  7: 0.004437298 -1.8423439 0.9718909 0.80502549
##  8: 0.004437298 -1.8423439 0.9718909 0.80502549
##  9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.004437298 -1.8423439 0.9718909 0.80502549
## 13: 0.004437298 -1.8423439 0.9718909 0.80502549
## 14: 0.004437298 -1.8423439 0.9718909 0.80502549
## 15: 0.004437298 -1.8423439 0.9718909 0.80502549
## 16: 0.004437298 -1.8423439 0.9718909 0.80502549
## 17: 0.004437298 -1.8423439 0.9718909 0.80502549
## 18: 0.004437298 -1.8423439 0.9718909 0.80502549
## 19: 0.004437298 -1.8423439 0.9718909 0.80502549
## 20: 0.004437298 -1.8423439 0.9718909 0.80502549
## 21: 0.004437298 -1.8423439 0.9718909 0.80502549
## 22: 0.004437298 -1.8423439 0.9718909 0.80502549
## 23: 0.004437298 -1.8423439 0.9718909 0.80502549
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.005027291 -1.1453678 0.6808478 0.04001638
## 27: 0.005027291 -1.1453678 0.6808478 0.04001638
## 28: 0.005027291 -1.1453678 0.6808478 0.04001638
## 29: 0.005027291 -1.1453678 0.6808478 0.04001638
## 30: 0.005027291 -1.1453678 0.6808478 0.04001638
## 31: 0.005027291 -1.1453678 0.6808478 0.04001638
## 32: 0.005027291 -1.1453678 0.6808478 0.04001638
## 33: 0.005027291 -1.1453678 0.6808478 0.04001638
## 34: 0.005027291 -1.1453678 0.6808478 0.04001638
## 35: 0.005027291 -1.1453678 0.6808478 0.04001638
## 36: 0.005027291 -1.1453678 0.6808478 0.04001638
## 37: 0.005027291 -1.1453678 0.6808478 0.04001638
## 38: 0.005027291 -1.1453678 0.6808478 0.04001638
## 39: 0.004876780 -1.6233205 0.9970391 0.31825293
## 40: 0.004876780 -1.6233205 0.9970391 0.31825293
## 41: 0.004864578 -1.8164413 1.1545088 0.27283204
## 42: 0.004864578 -1.8164413 1.1545088 0.27283204
## 43: 0.004864578 -1.8164413 1.1545088 0.27283204
## 44: 0.004864578 -1.8164413 1.1545088 0.27283204
## 45: 0.004864578 -1.8164413 1.1545088 0.27283204
## 46: 0.004864578 -1.8164413 1.1545088 0.27283204
## 47: 0.004864578 -1.8164413 1.1545088 0.27283204
## 48: 0.004864578 -1.8164413 1.1545088 0.27283204
## 49: 0.004864578 -1.8164413 1.1545088 0.27283204
## 50: 0.004864578 -1.8164413 1.1545088 0.27283204
## 51: 0.004864578 -1.8164413 1.1545088 0.27283204
## 52: 0.004864578 -1.8164413 1.1545088 0.27283204
## 53: 0.004864578 -1.8164413 1.1545088 0.27283204
## 54: 0.004864578 -1.8164413 1.1545088 0.27283204
## 55: 0.004864578 -1.8164413 1.1545088 0.27283204
## 56: 0.004864578 -1.8164413 1.1545088 0.27283204
## 57: 0.004864578 -1.8164413 1.1545088 0.27283204
## 58: 0.004864578 -1.8164413 1.1545088 0.27283204
## 59: 0.004864578 -1.8164413 1.1545088 0.27283204
## 60: 0.004864578 -1.8164413 1.1545088 0.27283204
## 61: 0.004864578 -1.8164413 1.1545088 0.27283204
## 62: 0.004864578 -1.8164413 1.1545088 0.27283204
## 63: 0.004864578 -1.8164413 1.1545088 0.27283204
## 64: 0.004541086 -0.4455417 1.1235184 0.24166784
## 65: 0.004541086 -0.4455417 1.1235184 0.24166784
## 66: 0.004541086 -0.4455417 1.1235184 0.24166784
## 67: 0.004541086 -0.4455417 1.1235184 0.24166784
## 68: 0.004541086 -0.4455417 1.1235184 0.24166784
## 69: 0.004541086 -0.4455417 1.1235184 0.24166784
## 70: 0.004541086 -0.4455417 1.1235184 0.24166784
## 71: 0.004541086 -0.4455417 1.1235184 0.24166784
## 72: 0.004541086 -0.4455417 1.1235184 0.24166784
## 73: 0.004541086 -0.4455417 1.1235184 0.24166784
## 74: 0.004541086 -0.4455417 1.1235184 0.24166784
## 75: 0.004541086 -0.4455417 1.1235184 0.24166784
## 76: 0.004541086 -0.4455417 1.1235184 0.24166784
## 77: 0.005235761 -1.1178069 0.8390202 0.58404011
## 78: 0.005006845 -1.4458246 0.9223899 0.99714609
## 79: 0.005006845 -1.4458246 0.9223899 0.99714609
##           se.bp          v         c       pchi

## [1] "ORF67_1" "ORF9"    "ORF73"   "ORF27"   "ORF32"   "ORF62"
## [1] 6
##  [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"
## [1] 13

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  2:       1    ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  3:       1   ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  4:       1   ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  5:       1   ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  6:       1   ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  7:       1   ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  8:       1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  9:       1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10:       1   ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11:       1  NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12:       2    ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 13:       2    ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 14:       2   ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 15:       2   ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 16:       2   ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 17:       2   ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 18:       2   ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 19:       2   ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 20:       2   ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 21:       2   ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 22:       2   ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 23:       2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 24:       2   ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25:       2   ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26:       3    ORF4 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 27:       3    ORF7 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 28:       3    ORF9 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 29:       3   ORF20 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 30:       3   ORF21 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 31:       3   ORF31 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 32:       3   ORF34 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 33:       3   ORF38 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 34:       3   ORF50 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 35:       3   ORF56 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 36:       3   ORF61 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 37:       3  NOIR_1 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 38:       4    ORF6 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 39:       4   ORF70 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 40:       5    ORF8 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 41:       5   ORF22 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 42:       5   ORF23 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 43:       5   ORF24 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 44:       5   ORF25 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 45:       5   ORF33 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 46:       5 ORF35.5 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 47:       5   ORF36 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 48:       5   ORF39 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 49:       5     CTO 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 50:       5   ORF40 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 51:       5   ORF42 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 52:       5   ORF43 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 53:       5   ORF44 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 54:       5   ORF46 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 55:       5   ORF49 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 56:       5   ORF58 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 57:       5   ORF62 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 58:       5   ORF68 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 59:       5   ORF74 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 60:       6   ORF12 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 61:       6   ORF13 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 62:       6   ORF15 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 63:       6   ORF16 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 64:       6   ORF35 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 65:       6   ORF41 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 66:       6   ORF48 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 67:       6   ORF52 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 68:       6   ORF54 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 69:       6   ORF57 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 70:       6   ORF60 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 71:       6   ORF71 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 72:       6   ORF72 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 73:       7   ORF27 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 74:       7   ORF32 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 75:       7   ORF59 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 76:       8   ORF28 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 77:       9   ORF45 0.5495521 0.9178209 0.3366369 0.043514069 0.0126360450
## 78:      10 ORF64_1 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## 79:      10   ORF75 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004437298 -1.8423439 0.9718909 0.80502549
##  2: 0.004437298 -1.8423439 0.9718909 0.80502549
##  3: 0.004437298 -1.8423439 0.9718909 0.80502549
##  4: 0.004437298 -1.8423439 0.9718909 0.80502549
##  5: 0.004437298 -1.8423439 0.9718909 0.80502549
##  6: 0.004437298 -1.8423439 0.9718909 0.80502549
##  7: 0.004437298 -1.8423439 0.9718909 0.80502549
##  8: 0.004437298 -1.8423439 0.9718909 0.80502549
##  9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.005027291 -1.1453678 0.6808478 0.04001638
## 13: 0.005027291 -1.1453678 0.6808478 0.04001638
## 14: 0.005027291 -1.1453678 0.6808478 0.04001638
## 15: 0.005027291 -1.1453678 0.6808478 0.04001638
## 16: 0.005027291 -1.1453678 0.6808478 0.04001638
## 17: 0.005027291 -1.1453678 0.6808478 0.04001638
## 18: 0.005027291 -1.1453678 0.6808478 0.04001638
## 19: 0.005027291 -1.1453678 0.6808478 0.04001638
## 20: 0.005027291 -1.1453678 0.6808478 0.04001638
## 21: 0.005027291 -1.1453678 0.6808478 0.04001638
## 22: 0.005027291 -1.1453678 0.6808478 0.04001638
## 23: 0.005027291 -1.1453678 0.6808478 0.04001638
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.004876780 -1.6233205 0.9970391 0.31825293
## 27: 0.004876780 -1.6233205 0.9970391 0.31825293
## 28: 0.004876780 -1.6233205 0.9970391 0.31825293
## 29: 0.004876780 -1.6233205 0.9970391 0.31825293
## 30: 0.004876780 -1.6233205 0.9970391 0.31825293
## 31: 0.004876780 -1.6233205 0.9970391 0.31825293
## 32: 0.004876780 -1.6233205 0.9970391 0.31825293
## 33: 0.004876780 -1.6233205 0.9970391 0.31825293
## 34: 0.004876780 -1.6233205 0.9970391 0.31825293
## 35: 0.004876780 -1.6233205 0.9970391 0.31825293
## 36: 0.004876780 -1.6233205 0.9970391 0.31825293
## 37: 0.004876780 -1.6233205 0.9970391 0.31825293
## 38: 0.004864578 -1.8164413 1.1545088 0.27283204
## 39: 0.004864578 -1.8164413 1.1545088 0.27283204
## 40: 0.004541086 -0.4455417 1.1235184 0.24166784
## 41: 0.004541086 -0.4455417 1.1235184 0.24166784
## 42: 0.004541086 -0.4455417 1.1235184 0.24166784
## 43: 0.004541086 -0.4455417 1.1235184 0.24166784
## 44: 0.004541086 -0.4455417 1.1235184 0.24166784
## 45: 0.004541086 -0.4455417 1.1235184 0.24166784
## 46: 0.004541086 -0.4455417 1.1235184 0.24166784
## 47: 0.004541086 -0.4455417 1.1235184 0.24166784
## 48: 0.004541086 -0.4455417 1.1235184 0.24166784
## 49: 0.004541086 -0.4455417 1.1235184 0.24166784
## 50: 0.004541086 -0.4455417 1.1235184 0.24166784
## 51: 0.004541086 -0.4455417 1.1235184 0.24166784
## 52: 0.004541086 -0.4455417 1.1235184 0.24166784
## 53: 0.004541086 -0.4455417 1.1235184 0.24166784
## 54: 0.004541086 -0.4455417 1.1235184 0.24166784
## 55: 0.004541086 -0.4455417 1.1235184 0.24166784
## 56: 0.004541086 -0.4455417 1.1235184 0.24166784
## 57: 0.004541086 -0.4455417 1.1235184 0.24166784
## 58: 0.004541086 -0.4455417 1.1235184 0.24166784
## 59: 0.004541086 -0.4455417 1.1235184 0.24166784
## 60: 0.005235761 -1.1178069 0.8390202 0.58404011
## 61: 0.005235761 -1.1178069 0.8390202 0.58404011
## 62: 0.005235761 -1.1178069 0.8390202 0.58404011
## 63: 0.005235761 -1.1178069 0.8390202 0.58404011
## 64: 0.005235761 -1.1178069 0.8390202 0.58404011
## 65: 0.005235761 -1.1178069 0.8390202 0.58404011
## 66: 0.005235761 -1.1178069 0.8390202 0.58404011
## 67: 0.005235761 -1.1178069 0.8390202 0.58404011
## 68: 0.005235761 -1.1178069 0.8390202 0.58404011
## 69: 0.005235761 -1.1178069 0.8390202 0.58404011
## 70: 0.005235761 -1.1178069 0.8390202 0.58404011
## 71: 0.005235761 -1.1178069 0.8390202 0.58404011
## 72: 0.005235761 -1.1178069 0.8390202 0.58404011
## 73: 0.005006845 -1.4458246 0.9223899 0.99714609
## 74: 0.005006845 -1.4458246 0.9223899 0.99714609
## 75: 0.005006845 -1.4458246 0.9223899 0.99714609
## 76: 0.005251022 -0.8623157 1.0323182 0.09873270
## 77: 0.004974233 -0.4844516 0.9061108 0.88802579
## 78: 0.005408057 -1.4764202 1.4415684 0.99966378
## 79: 0.005408057 -1.4764202 1.4415684 0.99966378
##           se.bp          v         c       pchi

## [1] "ORF55" "ORF73" "ORF62" "ORF27" "ORF32" "ORF59"
## [1] 6
##  [1] "ORF8"    "ORF22"   "ORF23"   "ORF24"   "ORF25"   "ORF33"   "ORF35.5"
##  [8] "ORF36"   "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"  
## [15] "ORF46"   "ORF49"   "ORF58"   "ORF62"   "ORF68"   "ORF74"   "ORF45"
## [1] 21

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  2:       1    ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  3:       1   ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  4:       1   ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  5:       1   ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  6:       1   ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  7:       1   ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  8:       1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  9:       1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10:       1   ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11:       1  NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12:       2    ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 13:       2    ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 14:       2   ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 15:       2   ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 16:       2   ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 17:       2   ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 18:       2   ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 19:       2   ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 20:       2   ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 21:       2   ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 22:       2   ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 23:       2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 24:       2   ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25:       2   ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26:       3    ORF4 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 27:       3    ORF9 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 28:       3   ORF20 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 29:       3   ORF21 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 30:       3   ORF31 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 31:       3   ORF34 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 32:       3   ORF38 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 33:       3   ORF50 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 34:       3   ORF61 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 35:       4    ORF6 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 36:       4   ORF70 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 37:       5    ORF7 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 38:       5   ORF56 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 39:       5  NOIR_1 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 40:       6    ORF8 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 41:       6   ORF22 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 42:       6   ORF23 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 43:       6   ORF24 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 44:       6   ORF25 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 45:       6   ORF33 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 46:       6 ORF35.5 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 47:       6   ORF36 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 48:       6   ORF39 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 49:       6     CTO 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 50:       6   ORF40 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 51:       6   ORF42 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 52:       6   ORF43 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 53:       6   ORF44 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 54:       6   ORF46 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 55:       6   ORF49 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 56:       6   ORF58 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 57:       6   ORF62 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 58:       6   ORF68 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 59:       6   ORF74 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 60:       7   ORF12 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 61:       7   ORF13 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 62:       7   ORF15 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 63:       7   ORF16 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 64:       7   ORF35 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 65:       7   ORF41 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 66:       7   ORF48 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 67:       7   ORF52 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 68:       7   ORF54 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 69:       7   ORF57 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 70:       7   ORF60 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 71:       7   ORF71 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 72:       7   ORF72 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 73:       8   ORF27 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 74:       8   ORF59 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 75:       9   ORF28 0.5495521 0.9178209 0.3366369 0.043514069 0.0126360450
## 76:      10   ORF32 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## 77:      11   ORF45 0.7410838 0.9752328 0.2580276 0.035672004 0.0053794818
## 78:      12 ORF64_1 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
## 79:      12   ORF75 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004437298 -1.8423439 0.9718909 0.80502549
##  2: 0.004437298 -1.8423439 0.9718909 0.80502549
##  3: 0.004437298 -1.8423439 0.9718909 0.80502549
##  4: 0.004437298 -1.8423439 0.9718909 0.80502549
##  5: 0.004437298 -1.8423439 0.9718909 0.80502549
##  6: 0.004437298 -1.8423439 0.9718909 0.80502549
##  7: 0.004437298 -1.8423439 0.9718909 0.80502549
##  8: 0.004437298 -1.8423439 0.9718909 0.80502549
##  9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.005027291 -1.1453678 0.6808478 0.04001638
## 13: 0.005027291 -1.1453678 0.6808478 0.04001638
## 14: 0.005027291 -1.1453678 0.6808478 0.04001638
## 15: 0.005027291 -1.1453678 0.6808478 0.04001638
## 16: 0.005027291 -1.1453678 0.6808478 0.04001638
## 17: 0.005027291 -1.1453678 0.6808478 0.04001638
## 18: 0.005027291 -1.1453678 0.6808478 0.04001638
## 19: 0.005027291 -1.1453678 0.6808478 0.04001638
## 20: 0.005027291 -1.1453678 0.6808478 0.04001638
## 21: 0.005027291 -1.1453678 0.6808478 0.04001638
## 22: 0.005027291 -1.1453678 0.6808478 0.04001638
## 23: 0.005027291 -1.1453678 0.6808478 0.04001638
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.004876780 -1.6233205 0.9970391 0.31825293
## 27: 0.004876780 -1.6233205 0.9970391 0.31825293
## 28: 0.004876780 -1.6233205 0.9970391 0.31825293
## 29: 0.004876780 -1.6233205 0.9970391 0.31825293
## 30: 0.004876780 -1.6233205 0.9970391 0.31825293
## 31: 0.004876780 -1.6233205 0.9970391 0.31825293
## 32: 0.004876780 -1.6233205 0.9970391 0.31825293
## 33: 0.004876780 -1.6233205 0.9970391 0.31825293
## 34: 0.004876780 -1.6233205 0.9970391 0.31825293
## 35: 0.004864578 -1.8164413 1.1545088 0.27283204
## 36: 0.004864578 -1.8164413 1.1545088 0.27283204
## 37: 0.004541086 -0.4455417 1.1235184 0.24166784
## 38: 0.004541086 -0.4455417 1.1235184 0.24166784
## 39: 0.004541086 -0.4455417 1.1235184 0.24166784
## 40: 0.005235761 -1.1178069 0.8390202 0.58404011
## 41: 0.005235761 -1.1178069 0.8390202 0.58404011
## 42: 0.005235761 -1.1178069 0.8390202 0.58404011
## 43: 0.005235761 -1.1178069 0.8390202 0.58404011
## 44: 0.005235761 -1.1178069 0.8390202 0.58404011
## 45: 0.005235761 -1.1178069 0.8390202 0.58404011
## 46: 0.005235761 -1.1178069 0.8390202 0.58404011
## 47: 0.005235761 -1.1178069 0.8390202 0.58404011
## 48: 0.005235761 -1.1178069 0.8390202 0.58404011
## 49: 0.005235761 -1.1178069 0.8390202 0.58404011
## 50: 0.005235761 -1.1178069 0.8390202 0.58404011
## 51: 0.005235761 -1.1178069 0.8390202 0.58404011
## 52: 0.005235761 -1.1178069 0.8390202 0.58404011
## 53: 0.005235761 -1.1178069 0.8390202 0.58404011
## 54: 0.005235761 -1.1178069 0.8390202 0.58404011
## 55: 0.005235761 -1.1178069 0.8390202 0.58404011
## 56: 0.005235761 -1.1178069 0.8390202 0.58404011
## 57: 0.005235761 -1.1178069 0.8390202 0.58404011
## 58: 0.005235761 -1.1178069 0.8390202 0.58404011
## 59: 0.005235761 -1.1178069 0.8390202 0.58404011
## 60: 0.005006845 -1.4458246 0.9223899 0.99714609
## 61: 0.005006845 -1.4458246 0.9223899 0.99714609
## 62: 0.005006845 -1.4458246 0.9223899 0.99714609
## 63: 0.005006845 -1.4458246 0.9223899 0.99714609
## 64: 0.005006845 -1.4458246 0.9223899 0.99714609
## 65: 0.005006845 -1.4458246 0.9223899 0.99714609
## 66: 0.005006845 -1.4458246 0.9223899 0.99714609
## 67: 0.005006845 -1.4458246 0.9223899 0.99714609
## 68: 0.005006845 -1.4458246 0.9223899 0.99714609
## 69: 0.005006845 -1.4458246 0.9223899 0.99714609
## 70: 0.005006845 -1.4458246 0.9223899 0.99714609
## 71: 0.005006845 -1.4458246 0.9223899 0.99714609
## 72: 0.005006845 -1.4458246 0.9223899 0.99714609
## 73: 0.005251022 -0.8623157 1.0323182 0.09873270
## 74: 0.005251022 -0.8623157 1.0323182 0.09873270
## 75: 0.004974233 -0.4844516 0.9061108 0.88802579
## 76: 0.005408057 -1.4764202 1.4415684 0.99966378
## 77: 0.004607497 -0.6572623 1.3067005 0.59272477
## 78: 0.004713028 -0.4001193 0.9858138 0.57239618
## 79: 0.004713028 -0.4001193 0.9858138 0.57239618
##           se.bp          v         c       pchi

## [1] "NOIR_2" "ORF1"   "ORF55"  "ORF73"  "ORF62"
## [1] 5
## [1] "ORF7"    "ORF56"   "NOIR_1"  "ORF28"   "ORF64_1" "ORF75"
## [1] 6

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  2:       1    ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  3:       1   ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  4:       1   ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  5:       1   ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  6:       1   ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  7:       1   ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  8:       1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
##  9:       1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10:       1   ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11:       1  NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12:       2    ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 13:       2    ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 14:       2   ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 15:       2   ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 16:       2   ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 17:       2   ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 18:       2   ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 19:       2   ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 20:       2   ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 21:       2   ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 22:       2   ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 23:       2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 24:       2   ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25:       2   ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26:       3    ORF4 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 27:       3    ORF9 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 28:       3   ORF20 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 29:       3   ORF21 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 30:       3   ORF31 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 31:       3   ORF34 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 32:       3   ORF38 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 33:       3   ORF50 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 34:       3   ORF61 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 35:       4    ORF6 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 36:       4   ORF70 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 37:       5    ORF7 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 38:       5   ORF56 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 39:       5  NOIR_1 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 40:       6    ORF8 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 41:       6   ORF22 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 42:       6   ORF23 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 43:       6   ORF24 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 44:       6   ORF25 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 45:       6   ORF33 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 46:       6 ORF35.5 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 47:       6   ORF36 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 48:       6   ORF39 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 49:       6     CTO 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 50:       6   ORF40 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 51:       6   ORF42 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 52:       6   ORF43 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 53:       6   ORF44 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 54:       6   ORF46 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 55:       6   ORF49 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 56:       6   ORF58 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 57:       6   ORF62 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 58:       6   ORF68 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 59:       6   ORF74 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 60:       7   ORF12 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 61:       7   ORF13 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 62:       7   ORF15 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 63:       7   ORF16 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 64:       7   ORF35 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 65:       7   ORF41 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 66:       7   ORF48 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 67:       7   ORF52 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 68:       7   ORF54 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 69:       7   ORF57 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 70:       7   ORF60 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 71:       7   ORF71 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 72:       7   ORF72 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 73:       8   ORF27 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 74:       8   ORF59 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 75:       9   ORF28 0.5495521 0.9178209 0.3366369 0.043514069 0.0126360450
## 76:      10   ORF32 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## 77:      11   ORF45 0.7410838 0.9752328 0.2580276 0.035672004 0.0053794818
## 78:      12 ORF64_1 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
## 79:      12   ORF75 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004437298 -1.8423439 0.9718909 0.80502549
##  2: 0.004437298 -1.8423439 0.9718909 0.80502549
##  3: 0.004437298 -1.8423439 0.9718909 0.80502549
##  4: 0.004437298 -1.8423439 0.9718909 0.80502549
##  5: 0.004437298 -1.8423439 0.9718909 0.80502549
##  6: 0.004437298 -1.8423439 0.9718909 0.80502549
##  7: 0.004437298 -1.8423439 0.9718909 0.80502549
##  8: 0.004437298 -1.8423439 0.9718909 0.80502549
##  9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.005027291 -1.1453678 0.6808478 0.04001638
## 13: 0.005027291 -1.1453678 0.6808478 0.04001638
## 14: 0.005027291 -1.1453678 0.6808478 0.04001638
## 15: 0.005027291 -1.1453678 0.6808478 0.04001638
## 16: 0.005027291 -1.1453678 0.6808478 0.04001638
## 17: 0.005027291 -1.1453678 0.6808478 0.04001638
## 18: 0.005027291 -1.1453678 0.6808478 0.04001638
## 19: 0.005027291 -1.1453678 0.6808478 0.04001638
## 20: 0.005027291 -1.1453678 0.6808478 0.04001638
## 21: 0.005027291 -1.1453678 0.6808478 0.04001638
## 22: 0.005027291 -1.1453678 0.6808478 0.04001638
## 23: 0.005027291 -1.1453678 0.6808478 0.04001638
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.004876780 -1.6233205 0.9970391 0.31825293
## 27: 0.004876780 -1.6233205 0.9970391 0.31825293
## 28: 0.004876780 -1.6233205 0.9970391 0.31825293
## 29: 0.004876780 -1.6233205 0.9970391 0.31825293
## 30: 0.004876780 -1.6233205 0.9970391 0.31825293
## 31: 0.004876780 -1.6233205 0.9970391 0.31825293
## 32: 0.004876780 -1.6233205 0.9970391 0.31825293
## 33: 0.004876780 -1.6233205 0.9970391 0.31825293
## 34: 0.004876780 -1.6233205 0.9970391 0.31825293
## 35: 0.004864578 -1.8164413 1.1545088 0.27283204
## 36: 0.004864578 -1.8164413 1.1545088 0.27283204
## 37: 0.004541086 -0.4455417 1.1235184 0.24166784
## 38: 0.004541086 -0.4455417 1.1235184 0.24166784
## 39: 0.004541086 -0.4455417 1.1235184 0.24166784
## 40: 0.005235761 -1.1178069 0.8390202 0.58404011
## 41: 0.005235761 -1.1178069 0.8390202 0.58404011
## 42: 0.005235761 -1.1178069 0.8390202 0.58404011
## 43: 0.005235761 -1.1178069 0.8390202 0.58404011
## 44: 0.005235761 -1.1178069 0.8390202 0.58404011
## 45: 0.005235761 -1.1178069 0.8390202 0.58404011
## 46: 0.005235761 -1.1178069 0.8390202 0.58404011
## 47: 0.005235761 -1.1178069 0.8390202 0.58404011
## 48: 0.005235761 -1.1178069 0.8390202 0.58404011
## 49: 0.005235761 -1.1178069 0.8390202 0.58404011
## 50: 0.005235761 -1.1178069 0.8390202 0.58404011
## 51: 0.005235761 -1.1178069 0.8390202 0.58404011
## 52: 0.005235761 -1.1178069 0.8390202 0.58404011
## 53: 0.005235761 -1.1178069 0.8390202 0.58404011
## 54: 0.005235761 -1.1178069 0.8390202 0.58404011
## 55: 0.005235761 -1.1178069 0.8390202 0.58404011
## 56: 0.005235761 -1.1178069 0.8390202 0.58404011
## 57: 0.005235761 -1.1178069 0.8390202 0.58404011
## 58: 0.005235761 -1.1178069 0.8390202 0.58404011
## 59: 0.005235761 -1.1178069 0.8390202 0.58404011
## 60: 0.005006845 -1.4458246 0.9223899 0.99714609
## 61: 0.005006845 -1.4458246 0.9223899 0.99714609
## 62: 0.005006845 -1.4458246 0.9223899 0.99714609
## 63: 0.005006845 -1.4458246 0.9223899 0.99714609
## 64: 0.005006845 -1.4458246 0.9223899 0.99714609
## 65: 0.005006845 -1.4458246 0.9223899 0.99714609
## 66: 0.005006845 -1.4458246 0.9223899 0.99714609
## 67: 0.005006845 -1.4458246 0.9223899 0.99714609
## 68: 0.005006845 -1.4458246 0.9223899 0.99714609
## 69: 0.005006845 -1.4458246 0.9223899 0.99714609
## 70: 0.005006845 -1.4458246 0.9223899 0.99714609
## 71: 0.005006845 -1.4458246 0.9223899 0.99714609
## 72: 0.005006845 -1.4458246 0.9223899 0.99714609
## 73: 0.005251022 -0.8623157 1.0323182 0.09873270
## 74: 0.005251022 -0.8623157 1.0323182 0.09873270
## 75: 0.004974233 -0.4844516 0.9061108 0.88802579
## 76: 0.005408057 -1.4764202 1.4415684 0.99966378
## 77: 0.004607497 -0.6572623 1.3067005 0.59272477
## 78: 0.004713028 -0.4001193 0.9858138 0.57239618
## 79: 0.004713028 -0.4001193 0.9858138 0.57239618
##           se.bp          v         c       pchi

## [1] "NOIR_2" "ORF1"   "ORF55"  "ORF73"  "ORF62"
## [1] 5
## [1] "ORF7"    "ORF56"   "NOIR_1"  "ORF28"   "ORF64_1" "ORF75"
## [1] 6

Remove genes from clusters ?

## [1] "ORF7"    "ORF56"   "NOIR_1"  "ORF28"   "ORF64_1" "ORF75"
## [1] 6
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    20
##  2:       2    14
##  3:       7    13
##  4:       1    11
##  5:       3     9
##  6:       5     3
##  7:       4     2
##  8:       8     2
##  9:      12     2
## 10:       9     1
## 11:      10     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters